E. coli MG1655 — genome-wide coherence pilot (results)

Generated by coherence_pilot.py. Numbers are computed live from the cached downloads; nothing here is hand-edited.

Inputs

• GO ontology: https://current.geneontology.org/ontology/go.obo (asserted has_part axioms)
• E. coli annotations: http://current.geneontology.org/annotations/ecocyc.gaf.gz (EcoCyc GAF)
• Directly annotated GO terms (non-NOT): 4120 (4119 resolvable & non-obsolete)
• Present set after is_a+part_of closure: 5507 classes
• Asserted has_part pairs in GO: 743

Coherence

• Activated dependencies (whole present in genome): 129
• Unsatisfied (required part absent): 17
• Coherence = 86.8%

Each unsatisfied dependency is a reviewable lead — a process annotated in the genome whose required part is annotated on no protein. See violations.tsv for the full list. Top examples:

• GO:0000910 cytokinesis has_part GO:0090148 membrane fission — part not present
• GO:0001070 RNA-binding transcription regulator activity has_part GO:0001068 transcription regulatory region RNA binding — part not present
• GO:0001680 tRNA 3'-terminal CCA addition has_part GO:0052927 CC tRNA cytidylyltransferase activity — part not present
• GO:0001680 tRNA 3'-terminal CCA addition has_part GO:0052929 ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity — part not present
• GO:0006413 translational initiation has_part GO:0001677 formation of translation initiation ternary complex — part not present
• GO:0016579 protein deubiquitination has_part GO:0004843 cysteine-type deubiquitinase activity — part not present
• GO:0017089 glycolipid transfer activity has_part GO:0051861 glycolipid binding — part not present
• GO:0019062 virion attachment to host cell has_part GO:0046812 host cell surface binding — part not present
• GO:0019333 denitrification pathway has_part GO:0050304 nitrous-oxide reductase activity — part not present
• GO:0031507 heterochromatin formation has_part GO:0033696 heterochromatin boundary formation — part not present
• GO:0032324 molybdopterin cofactor biosynthetic process has_part GO:0061604 molybdopterin-synthase sulfurtransferase activity — part not present
• GO:0046813 receptor-mediated virion attachment to host cell has_part GO:0005102 signaling receptor binding — part not present
• GO:0075713 establishment of integrated proviral latency has_part GO:0044826 viral genome integration into host DNA — part not present
• GO:0098552 side of membrane has_part GO:0097478 leaflet of membrane bilayer — part not present
• GO:1990100 DnaB-DnaC complex has_part GO:1990161 DnaB helicase complex — part not present

Illustrative completeness probe (sanity check, not the metric)

• ✓ GO:0006260 DNA replication
• ✓ GO:0006351 DNA-templated transcription
• ✓ GO:0006412 translation
• ✓ GO:0009058 biosynthetic process
• ✓ GO:0006096 glycolytic process

Caveats

• Asserted has_part only; the reference paper adds ELK-inferred pairs (~5038). A low count here reflects GO's sparse asserted process-level has_part, so coherence is a lower bound on detectable violations.
• A violation can be a genuine biological gap or a missing annotation (this check never looks at sequence). Resolve flagged gaps with a sequence-level tool (GapMind / Pathway Tools) before acting.